# Run all clades once
**URL:** https://forum.biobakery.org/t/run-all-clades-once/1799
**Category:** StrainPhlAn
**Created:** [March 16, 2021, 8:23pm UTC](https://forum.biobakery.org/t/run-all-clades-once/1799 "2021-03-16T20:23:28Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@farmer2020](https://forum.biobakery.org/u/farmer2020)
#### Post date: [March 16, 2021, 8:23pm UTC](https://forum.biobakery.org/t/run-all-clades-once/1799/1 "2021-03-16T20:23:28Z")
Hello,
I am moving from StrainPhlAn2 to StrainPhlAn3, and one question is whether flag --clade in StrainPhlAn3 is mandatory or not? If yes, and I want to investigate all clades without defining specific extracted markers from MetaPhlAn database and reference-genomes, what shoud I do?
strainphlan -s consensus\_markers/\*.pkl -o output -n 8 -c **xxx?** --phylophlan\_mode accurate --mutation\_rates
Many thanks
Wang
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### Author:  [@farmer2020](https://forum.biobakery.org/u/farmer2020)
#### Post date: [March 19, 2021, 5:20pm UTC](https://forum.biobakery.org/t/run-all-clades-once/1799/2 "2021-03-19T17:20:43Z")
Hi, may I get the answer to my question as above? Many thanks.
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### Author:  [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)
#### Post date: [March 19, 2021, 5:34pm UTC](https://forum.biobakery.org/t/run-all-clades-once/1799/3 "2021-03-19T17:34:01Z")
Hi @farmer2020
Sorry for the late response. Yes, the `--clade` parameter is mandatory when StrainPhlAn3 is executed. If you want to know all the available species StrainPhlAn is able to profile from your samples, you can use the parameter `--print_clades_only` as follows:
`strainphlan -s consensus_markers/*.pkl -o output --print_clades_only`
Then, you can run StrainPhlAn for each of your clades individually.
Best
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### Author:  [@farmer2020](https://forum.biobakery.org/u/farmer2020)
#### Post date: [March 19, 2021, 5:46pm UTC](https://forum.biobakery.org/t/run-all-clades-once/1799/4 "2021-03-19T17:46:39Z")
So is it not possible to run all the clades at one time?
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### Author:  [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)
#### Post date: [March 19, 2021, 5:58pm UTC](https://forum.biobakery.org/t/run-all-clades-once/1799/5 "2021-03-19T17:58:11Z")
No, in the new version each clade has to be runned independenly.
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### Author:  [@farmer2020](https://forum.biobakery.org/u/farmer2020)
#### Post date: [March 19, 2021, 6:30pm UTC](https://forum.biobakery.org/t/run-all-clades-once/1799/6 "2021-03-19T18:30:35Z")
Okay, many thanks. Best, Wang